Protein profile

KP13_01277

Anaerobic ribonucleoside-triphosphate reductase-activating protein

Genome: KpKP13

Gene: nrdG AHE46657.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GIA9
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Amino acids 154
Annotations 7
Features 16
PDB binders 1
Druggability 0.393

Overview

Basic information about this protein and its source genome.

Accession
KP13_01277
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
nrdG AHE46657.1
Status
annotated
Amino acids
154
Structure source
AlphaFold + ColabFold
EC
1.97.1.-
GO
GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. GO:0043365 Catalysis of the reaction: S-adenosyl-L-methionine + dihydroflavodoxin + [formate C-acetyltransferase]-glycine = 5'-deoxyadenosine + L-methionine + flavodoxin semiquinone + [formate C-acetyltransferase]-glycin-2-yl radical. GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0046872 Binding to a metal ion. GO:0004748 Catalysis of the reaction: 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin. Thioredoxin disulfide is the oxidized form of thioredoxin.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
97.28

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.393
Structure A0A0H3GIA9
Pocket Pocket 1
P2Rank 0.789
Structure A0A0H3GIA9
Pocket Pocket 1
ColabFold model
FPocket 0.952 · Pocket 2
P2Rank 0.873 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 143 / 4744 genomes with a hit
Normalized 0.03

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0043365 Catalysis of the reaction: S-adenosyl-L-methionine + dihydroflavodoxin + [formate C-acetyltransferase]-glycine = 5'-deoxyadenosine + L-methionine + flavodoxin semiquinone + [formate C-acetyltransferase]-glycin-2-yl radical.
  • GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0046872 Binding to a metal ion.
  • GO:0004748 Catalysis of the reaction: 2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin. Thioredoxin disulfide is the oxidized form of thioredoxin.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
1 153 SFLD SFLDF00299 anaerobic ribonucleoside-triphosphate reductase activase
1 153 InterPro IPR012837 Ribonucleoside-triphosphate reductase activating, anaerobic
12 151 Pfam PF13353 4Fe-4S single cluster domain
2 153 Gene3D G3DSA:3.20.20.70 Aldolase class I
2 153 InterPro IPR013785 Aldolase-type TIM barrel
14 35 ProSitePatterns PS01087 Radical activating enzymes signature.
14 35 InterPro IPR001989 Radical-activating enzyme, conserved site
16 114 SUPERFAMILY SSF102114 Radical SAM enzymes
1 154 PIRSF PIRSF000368 Anaer_RNR_III_small
1 154 InterPro IPR012837 Ribonucleoside-triphosphate reductase activating, anaerobic
2 151 PANTHER PTHR30352 PYRUVATE FORMATE-LYASE-ACTIVATING ENZYME
2 151 InterPro IPR034457 Organic radical-activating enzymes
2 153 NCBIfam TIGR02491 anaerobic ribonucleoside-triphosphate reductase activating protein
2 153 InterPro IPR012837 Ribonucleoside-triphosphate reductase activating, anaerobic
1 153 SFLD SFLDG01066 organic radical-activating enzymes
2 153 FunFam G3DSA:3.20.20.70:FF:000087 Anaerobic ribonucleoside-triphosphate reductase-activating protein

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GIA9
AlphaFold — — full sequence — Viewing
ColabFold KP13_01277
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
1 0.393
6 0.232

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 14.82 0.735

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

1 records

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
MT2
3C8F
P0A9N4 178.3 Da LogP 0.06 TPSA 63.3 ✓ Ro5 ✓ Clean CC[S@@+](C)CC[C@@H](C(=O)O)N

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.